A deeper look at the carrier proteome effect on D20 Orbitrap systems!

 

Do you have a high field D20 Orbitrap system and are considering SCoPE-MS or BOOST type strategies to dig into single cells or phosphotyrosines or just general low abundance signal? 

Would you like another look into the limits where things your quan gets wonky on these instruments? You're in luck! 

The most interesting points of this study (for me) are the specific distortions that are noted in particular channels and some new insight on the collision energies that should be used for MS2 based quantification.

I will (again) issue some caution here that this study, like a couple before it, are largely defining the carrier proteome limits for one hardware configuration, the high field (or ultra high field? I forget) D20 Orbitrap. (Exploris, Fusion 1-3, maybe HF and HF-X?) 

In my always humble opinion, these results should not be directly extrapolated or implied to be universal for other pieces of hardware. In all honesty, I don't think that these results should even be considered to be directly applicable to the significantly larger D30 Orbitrap systems (Q Exactive/ QE Plus, etc.,), which may clear up some slightly different numbers for carrier proteome effects between a QE Classic and the Exploris and Fusion systems that we've seen. The carrier proteome effect is a direct function of multiple instrument factors, most notably the ion capacity of the instrument and the intrascan linear dynamic range of the mass analyzer itself. 

In an extreme example, (again, humbly submitted) it would be just silly to assume that quan would get wonky on a triple quad instrument which has 6 orders of effective intrascan linear dynamic range and does not trap or store ions, based on these data. 

However, as the clearly dominant technology in LCMS based proteomics today is the amazing D20 Orbitrap due to the ability to massively multiplex and the fact they are coupled to pretty fantastic quads (and, increasingly, to rapidly improving FAIMS separations) it makes a ton of sense to really dig into this. The D20 Orbitraps aren't going anywhere and it's great to know the limits of this hardware configuation for this approach.